Ab initio study of MKr(n)²⁺(M = Cu, Ag, and Au, n = 1-6) clusters.

abstract：:Bacterial cytidylate kinase or cytidine monophosphate kinase (CMP kinase) catalyses the phosphoryl transfer from ATP to CMP and dCMP, resulting in the formation nucleoside diphosphates. In eukaryotes, CMP/UMP kinase catalyses the conversion of UMP and CMP to, respectively, UDP and CDP with high efficiency. This work d...

journal_title：Journal of molecular modeling

authors： Caceres RA,Macedo Timmers LF,Vivan AL,Schneider CZ,Basso LA,De Azevedo WF Jr,Santos DS

更新日期：2008-05-01 00:00:00

abstract：:Several noble-gas-containing molecules XNgY were observed experimentally. However, the bonding in such systems is still not understood. Using natural bond orbital and natural resonance theory (NBO/NRT) methods, the present work investigated bonding of the title molecules. The results show that each of the studied XNgY...

journal_title：Journal of molecular modeling

authors： Song J,Su Y,Jia Y,Chen L,Zhang G

更新日期：2018-05-07 00:00:00

abstract：:Paracetamol is a relatively safe analgesia/antipyretic drug without the risks of addiction, dependence, tolerance, and withdrawal when used alone. However, when administrated in an opioid/paracetamol combination product, which often contains a large quantity of paracetamol, it can be potentially dangerous due to the r...

journal_title：Journal of molecular modeling

authors： Wang Y,Lin W,Wu N,He X,Wang J,Feng Z,Xie XQ

更新日期：2018-08-18 00:00:00

abstract：:Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To addres...

journal_title：Journal of molecular modeling

authors： Gao J,Cui W,Du Y,Ji M

更新日期：2013-12-01 00:00:00

abstract：:A theoretical study of the sulfur cumulenes SCnS (n = 3-8), CnS ( n = 1-8) and of their protonated forms (SCnS)H(+) and (CnS)H(+) that might exist in the interstellar environment, has been carried out by means of the standard B3LYP/6-311G** method. The geometries and relative energies of singlet and triplet states acc...

journal_title：Journal of molecular modeling

authors： Benmensour MA,Djennane-Bousmaha S,Boucekkine A

更新日期：2014-07-01 00:00:00

abstract：:White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (desi...

journal_title：Journal of molecular modeling

authors： Jamalpure S,Panditrao G,Kulabhusan PK,Hameed ASS,Paknikar KM,Joshi M,Rajwade JM

更新日期：2020-09-10 00:00:00

abstract：:The geometric and electronic structures, absorption spectra, transporting properties, chemical reactivity indices and electrostatic potentials of the planar three-coordinate organoboron compounds 1-2 and twisted reference compound Mes(3)B, have been investigated by employing density functional theory (DFT) and concept...

journal_title：Journal of molecular modeling

authors： Jin JL,Li HB,Lu T,Duan YA,Geng Y,Wu Y,Su ZM

更新日期：2013-08-01 00:00:00

abstract：:Hydrogen dissociative chemisorption and desorption on small lowest energy Ni(n) clusters up to n=13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy pat...

journal_title：Journal of molecular modeling

authors： Zhou C,Yao S,Zhang Q,Wu J,Yang M,Forrey RC,Cheng H

更新日期：2011-09-01 00:00:00

abstract：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...

journal_title：Journal of molecular modeling

authors： Victor Paul Raj FR,Exner TE

更新日期：2014-04-01 00:00:00

abstract：:Recently, both lithium (Li) salts and Li electrides formed by one Li atom interacting with ligand complexes, have been widely investigated. An interesting question emerges: is the configuration of one Li atom interacting with ligand complexes a Li salt or electride? In the present work, four configurations n-Li-PNA (n...

journal_title：Journal of molecular modeling

authors： Gao Y,Wu HQ,Sun SL,Xu HL,Su ZM

更新日期：2015-02-01 00:00:00

abstract：:The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concen...

journal_title：Journal of molecular modeling

authors： Pospísil M,Capková P,Weissmannová H,Klika Z,Trchová M,Chmielová M,Weiss Z

更新日期：2003-02-01 00:00:00

abstract：:The cold shock protein from the hyperthermophile Thermotoga maritima (Tm-Csp) exhibits significantly higher thermostability than its homologue from the thermophile Bacillus caldolyticus (Bc-Csp). Experimental studies have shown that the electrostatic interactions unique to Tm-Csp are responsible for improving its ther...

journal_title：Journal of molecular modeling

authors： Su JG,Han XM,Zhao SX,Hou YX,Li XY,Qi LS,Wang JH

更新日期：2016-04-01 00:00:00

abstract：:We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-...

journal_title：Journal of molecular modeling

authors： Dzwinel W,Yuen DA,Boryczko K

更新日期：2002-01-01 00:00:00

abstract：:There is a wide variety of ion channel types with various types of blockers, making research in this field very complicated. To reduce this complexity, it is essential to study ion channels and their blockers independently. Scorpion toxins, a major class of blockers, are charged short peptides with high affinities for...

journal_title：Journal of molecular modeling

authors： Nikouee A,Khabiri M,Cwiklik L

更新日期：2015-11-01 00:00:00

abstract：:Compound P131 has been established to inhibit Cryptosporidium parvum's inosine monophosphate dehydrogenase (CpIMPDH). Its inhibitory activity supersedes that of paromomycin, which is extensively used in treating cryptosporidiosis. Through the per-residue energy decomposition approach, crucial moieties of P131 were ide...

journal_title：Journal of molecular modeling

authors： Omolabi KF,Iwuchukwu EA,Agoni C,Olotu FA,Soliman MES

更新日期：2021-01-09 00:00:00

abstract：:The reactivity of the 5-arylidenerhodanine and 5-arylideneisorhodanine derivatives in reactions with dimethyl maleate was computationally studied at the DFT(M06-2X)/6-311+G(d,p) theory level. Eight stereoisomers of the reaction products were considered. The effect of the solvent was taken into account by means of the ...

journal_title：Journal of molecular modeling

authors： Tejchman W,Michalski M,Zborowski KK,Berski S

更新日期：2019-06-14 00:00:00

abstract：:Temperature dependences of the spontaneous polarization and the dielectric constant are calculated near the paraelectric-ferroelectric (cubic-tetragonal) transition in BaTiO3 using our mean field model. By expanding the free energy in terms of the spontaneous polarization (order parameter), expressions for the tempera...

journal_title：Journal of molecular modeling

authors： Yurtseven H,Kiraci A

更新日期：2013-09-01 00:00:00

abstract：:Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding thei...

journal_title：Journal of molecular modeling

authors： Armaković S,Armaković SJ,Abramović BF

更新日期：2016-10-01 00:00:00

abstract：:The double-histone fold is a rare protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus giving a histone pseudodimer. Previously, this fold was found in a few prokaryotic histones and in the regulatory region of guanine-nucleotide exchange factors of t...

journal_title：Journal of molecular modeling

authors： Greco C,Sacco E,Vanoni M,De Gioia L

更新日期：2005-12-01 00:00:00

abstract：:In this work a molecular modeling study was carried out based on a series of organotin(IV) derivatives which were complexed with ONO-Donor type Schiff base ligands to build up a statistical data pool for researchers. For this purpose, various properties of the selected complexes such as energies, band gaps, chemical r...

journal_title：Journal of molecular modeling

authors： Şirikci G,Ancın NA,Öztaş SG

更新日期：2015-09-01 00:00:00

abstract：:The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range additio...

journal_title：Journal of molecular modeling

authors： Guseinov II,Görgün NS

更新日期：2011-06-01 00:00:00

abstract：:The Z-DNA-binding domain of human double-stranded RNA adenosine deaminase I (hZαADAR1) can specifically recognize the left-handed Z-DNA which preferentially occurs at alternating purine-pyrimidine repeats, especially the CG-repeats. The interactions of hZαADAR1 and Z-DNAs in different sequence contexts can affect many...

journal_title：Journal of molecular modeling

authors： Wang Q,Li L,Wang X,Liu H,Yao X

更新日期：2014-11-01 00:00:00

abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...

journal_title：Journal of molecular modeling

authors： Latosińska JN,Latosińska M,Tomczak MA,Seliger J,Zagar V

更新日期：2011-07-01 00:00:00

abstract：:Mechanisms for the activation of water, ammonia, and other small molecules by the PCcarbeneP nickel pincer complex were studied computationally with the aid of density functional theory. The calculation results indicate that the strongly donating, nucleophilic carbene center can engage in a variety of heterolytic spli...

journal_title：Journal of molecular modeling

authors： Liu CC,Liu QL,Wu ZY,Chen YC,Xie HJ,Lei QF,Fang WJ

更新日期：2015-09-01 00:00:00

abstract：:The structures of the 4,4',4″-tris(N,N-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer in their neutral and positively charged forms were studied by performing quantum-chemical calculations at the Hartree-Fock (HF) and density functional theory (DFT) levels of theory using several exchange-...

journal_title：Journal of molecular modeling

authors： Safonov A,Rykova E,Bagaturyants A

更新日期：2018-11-28 00:00:00

abstract：:The biological toxicity of uranyl ion (UO (2) (2+) ) lies in interacting with proteins and disrupting their native functions. The structural and functional consequences of UO (2) (2+) interacting with cytochrome b (5) (cyt b (5)), a small membrane heme protein, and its heme axial ligand His39Ser variant, cyt b (5) H39...

journal_title：Journal of molecular modeling

authors： Wan D,Liao LF,Zhao MM,Wu ML,Wu YM,Lin YW

更新日期：2012-03-01 00:00:00

abstract：:Ergothioneine (2-mercaptohistidine trimethylbetaine) is a very stable natural compound largely present in cells and tissues of plants and mammals. The biological role of ET is still incompletely understood but its antioxidant properties are well assessed experimentally. However, no theoretical study had been performed...

journal_title：Journal of molecular modeling

authors： Lespade L

更新日期：2019-10-26 00:00:00

abstract：:Theoretical adiabatic electron affinities are often considered inaccurate because they are referenced to only a single value. Ground state electron affinities for all the main group elements and homonuclear diatomics were identified recently using the normalized binding energy of the hydrogen atom: [0.75420375(3)/2 = ...

journal_title：Journal of molecular modeling

authors： Chen ES,Keith H,Lim T,Pham D,Rosenthal R,Herder C,Pai S,Flores RA,Chen EC

更新日期：2015-04-01 00:00:00

abstract：:The unusual π-halogen bond interactions are investigated between (BNN)₃⁺ and X1X2 (X1, X2 = F, Cl, Br) employing MP2 at 6-311 + G(2d) and aug-cc-pVDZ levels according to the "CP (counterpoise) corrected potential energy surface (PES)" method. The order of the π-halogen bond interactions and stabilities of the complexe...

journal_title：Journal of molecular modeling

authors： Qi HT,Ren FD,Zhang JL,Wang JY

更新日期：2011-05-01 00:00:00

abstract：:Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and...

journal_title：Journal of molecular modeling

authors： Gaete-Eastman C,Morales-Quintana L,Herrera R,Moya-León MA

更新日期：2015-05-01 00:00:00